Ragulating chromatin structures by manipulating chromatin loops

• Project/Area Number: 25650014
• Research Category: Grant-in-Aid for Challenging Exploratory Research
• Allocation Type: Multi-year Fund
• Research Field: Molecular biology
• Research Institution: Tokyo Metropolitan Institute of Medical Science
• Principal Investigator: MASAI Hisao 公益財団法人東京都医学総合研究所, ゲノム医科学研究分野, 副所長 (40229349)
• Project Period (FY): 2013-04-01 – 2016-03-31
• Project Status: Completed (Fiscal Year 2015)
• Budget Amount: ¥4,160,000 (Direct Cost: ¥3,200,000、Indirect Cost: ¥960,000); Fiscal Year 2015: ¥910,000 (Direct Cost: ¥700,000、Indirect Cost: ¥210,000); Fiscal Year 2014: ¥1,690,000 (Direct Cost: ¥1,300,000、Indirect Cost: ¥390,000); Fiscal Year 2013: ¥1,560,000 (Direct Cost: ¥1,200,000、Indirect Cost: ¥360,000)
• Keywords: Rif1タンパク質 / クロマチンループ / 核内染色体構造 / 複製タイミング / グアニン4重鎖構造 / 核膜 / グアニン４重鎖構造 / 転写 / 染色体核内配置 / Rif1 / タンパク質 / 組換え

Outline of Final Research Achievements

We try to develop a novel method by which to manipulate chromatin loop structures by using a conserved nuclear protein, Rif1. Rif1 was shown to regulate DNA replication timing domains through facilitating formation of chromatin loops. Fission yeast Rif1 binds specifically to G-quadruplex (G4) structures through its C-terminal 271 aa segment and conserved amino acids near its C-terminus are required for both its DNA binding and oligomerization. Overexpression of Rif1 in fission yeast induced aberrant chromatin structures and growth inhibition. Growth inhibition did not require its PP1 binding but required DNA binding activity. Based on the target preference of Rif1 protein, we are now manipulating chromatin structures and activities by introducing high-affinity Rif1 target G4 sequences at specific locations on the chromosomes.

Research Products

• [Journal Article] Characterization of conserved arginine residues on Cdt1 that affect licensing activity and interaction with Geminin or Mcm complex. (2016)
  • Author(s): Zhiying You, Koji L. Ode, Haruhiko Takisawa, and *Hisao Masai
  • Journal Title: Cell Cycle Volume: 3
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Fork restart protein, PriA, binds around oriC after depletion of nucleotide precursors: Replication fork arrest near the replication origin. (2016)
  • Author(s): Tanaka T, Nishito Y, *Masai H.
  • Journal Title: Biochem. Biophys. Res. Commun. Volume: 470 Issue: 3 Pages: 546-551
  • DOI: 10.1016/j.bbrc.2016.01.108
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Epigenetic Regulation of the Blimp-1 Gene (Prdm1) in B Cells Involves Bach2 and Histone Deacetylase 3* (2016)
  • Author(s): Tanaka H
  • Journal Title: JBC Volume: 291 Issue: 12 Pages: 6316-6330
  • DOI: 10.1074/jbc.m116.713842
  • Peer Reviewed / Open Access / Int'l Joint Research
• [Journal Article] Phosphorylation of TAR DNA-binding Protein of 43 kDa (TDP-43) by Truncated Casein Kinase 1δ Triggers Mislocalization and Accumulation of TDP-43. (2016)
  • Author(s): Nonaka T, Suzuki G, Tanaka Y, Kametani F, Hirai S, Okado H, Miyashita T, Saitoe M, Akiyama H, Masai H, Hasegawa M.
  • Journal Title: The journal of Biological Chemistry Volume: 291 Issue: 11 Pages: 5473-83
  • DOI: 10.1074/jbc.m115.695379
  • Peer Reviewed / Open Access
• [Journal Article] Claspin recruits Cdc7 kinase for initiation of DNA replication in human cells. (2016)
  • Author(s): Chi-Chun Yang, Masahiro Suzuki, Shiori Yamakawa, Syuzi Uno, Ai Ishii, Satoshi Yamazaki, Rino Fukatsu, Ryo Fujisawa, Kenji Sakimura3, Toshiki Tsurimoto, *Hisao Masai
  • Journal Title: Nature Communications Volume: TBA
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Rif1はグアニン４重鎖構造を介して染色体に結合し、広範囲に複製を抑制する (2016)
  • Author(s): 加納 豊、松本 清治、正井 久雄
  • Journal Title: 実験医学 Volume: 34-no.3 Pages: 458-461
  • Acknowledgement Compliant
• [Journal Article] CDC28 phosphorylates Cac1p and regulates the association of Chromatin Assembly Factor I with chromatin. (2015)
  • Author(s): Jeffery, D., Kakusho, N., You, Z., Gharib, M., Wyse, B., Drury, E., Weinreich, M., Thibault, P. Verreault, A., Masai, H. and *Yankulov, K.
  • Journal Title: Cell Cycle Volume: 14 Issue: 1 Pages: 74-85
  • DOI: 10.4161/15384101.2014.973745
  • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Definition of the transcription factor TdIF1 consensus binding sequence through genome-wide mapping of its binding sites. (2015)
  • Author(s): Kotaro Koiwai, Takashi Kubota, Nobuhisa Watanabe, Katsutoshi Hori, Osamu Koiwai and Hisao Masai
  • Journal Title: Genes to Cells Volume: 20 Issue: 3 Pages: 242-254
  • DOI: 10.1111/gtc.12216
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] The DNA-Binding Domain of S. pombe Mrc1 (Claspin) Acts to Enhance Stalling at Replication Barriers. (2015)
  • Author(s): Zech, J., Godfrey, E.L., Masai, H., Hartsuiker, E. and *Dalgaard, J.Z.
  • Journal Title: PLoS One Volume: 10 Issue: 7 Pages: e0132595-e0132595
  • DOI: 10.1371/journal.pone.0132595
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] BTB-ZF Protein Znf131 Regulates Cell Growth of Developing and Mature T Cells. (2015)
  • Author(s): Iguchi T, Aoki K, Ikawa T, Taoka M, Taya C, Yoshitani H, Toma-Hirano M, Koiwai O, Isobe T, Kawamoto H, Masai H, Miyatake S.
  • Journal Title: The Journal of Immunology Volume: 195 Issue: 3 Pages: 982-93
  • DOI: 10.4049/jimmunol.1500602
  • Peer Reviewed / Acknowledgement Compliant
• [Journal Article] Rif1 binds to G-quadruplexes and suppresses replication over long distances. (2015)
  • Author(s): Yutaka Kanoh, Seiji Matsumoto, Rino Fukatsu, Naoko Kakusho, Nobuaki Kono, Claire Renard-Guillet, Koji Masuda, Keisuke Iida, Kazuo Nagasawa, Katsuhiko Shirahige, and *Hisao Masai
  • Journal Title: Nature Struct. Mol. Biol. Volume: 22 Issue: 11 Pages: 889-897
  • DOI: 10.1038/nsmb.3102
  • Peer Reviewed / Open Access / Int'l Joint Research / Acknowledgement Compliant
• [Journal Article] Rif1はグアニン4重鎖構造を形成するDNAを介して染色体へ結合し複製の開始を広範囲にわたり抑制する (2015)
  • Author(s): 加納 豊、松本 清治、正井 久雄
  • Journal Title: ライフサイエンス 新着論文レビュー Volume: -
• [Journal Article] NCOA4 Transcriptional Coactivator Inhibits Activation of DNA Replication Origins. (2014)
  • Author(s): Bellelli, R., Castellone, M.D., Guida, T., Limongello, R., Dathan, N.A., Merolla, F., Cirafici, A.M., Affuso, A., Masai, H., Costanzo, V., Grieco, D., Fusco, A., Santoro, M., and Carlomagno, F.
  • Journal Title: Mol. Cell Volume: 55 Issue: 1 Pages: 123-137
  • DOI: 10.1016/j.molcel.2014.04.031
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Regulation and roles of Cdc7 kinase under replication stress. (2014)
  • Author(s): Yamada, M., Masai, H., and Bartek, J.
  • Journal Title: Cell Cycle Volume: 13 Issue: 12 Pages: 1859-1866
  • DOI: 10.4161/cc.29251
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Cell cycle synchronization and flow cytometry analysis of mammalian cell. (2014)
  • Author(s): Yoshizawa-Sugata, N. and Masai, H.
  • Journal Title: Methods in Molecular Biology Volume: 1170 Pages: 279-293
  • DOI: 10.1007/978-1-4939-0888-2_13
  • ISBN: 9781493908875, 9781493908882
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] ATM in prevention of genomic instability. (2014)
  • Author(s): Hisao Masai
  • Journal Title: Cell Cycle Volume: 13 Issue: 6 Pages: 882-883
  • DOI: 10.4161/cc.28216
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Temporal and spatial regulation of eukaryotic DNA replication: from regulated initiation to genome-scale timing program. (2014)
  • Author(s): Renard-Guillet, C., Kanoh, Y., Shirahige, K., and Masai, H.
  • Journal Title: Seminars in Cell & Developmental Biology, Volume: 30 Pages: 110-120
  • DOI: 10.1016/j.semcdb.2014.04.014
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] "Cell cycle synchronization and flow cytometry analysis of mammalian cell." (2014)
  • Author(s): Yoshizawa-Sugata, N. and Masai, H
  • Journal Title: Methods in Molecular Biology Volume: in press
  • Peer Reviewed
• [Journal Article] ATR-Chk1-APC/CCdh1-dependent stabilization of Cdc7-ASK(Dbf4) kinase complex is required for DNA damage bypass under replication stress. (2013)
  • Author(s): Yamada, M., Watanabe, K., Mistrik, M., Mailand, N., Lee, M-H., Masai, H., Lukas, J. and Bartek, B.
  • Journal Title: Genes and Development Volume: 27 Issue: 22 Pages: 2459-72
  • DOI: 10.1101/gad.224568.113
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] "MCM helicase interacts with primase and stimulates its priming activity." (2013)
  • Author(s): You, Z., De Falco, S., Pisani, F.M. and Masai, H
  • Journal Title: PLoS One Volume: 8 Issue: 8 Pages: e72408-e72408
  • DOI: 10.1371/journal.pone.0072408
  • Peer Reviewed
• [Journal Article] The Human Tim/Tipin Complex Directly Interacts with DNA Polymerase {epsilon} and Stimulates its Synthetic Activity. (2013)
  • Author(s): Aria, V., De Felice, M., Di Perna, R., Uno, S., Masai, H., Syvaoja, J.E., van Loon, B., Hubscher, U. and Pisani, F.M.
  • Journal Title: J. Biol. Chem. Volume: 288 Issue: 18 Pages: 12742-12752
  • DOI: 10.1074/jbc.m112.398073
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation. (2013)
  • Author(s): Jeffery, D.C., Wyse, B.A., Rehman, M.A., Brown, G.W., You, Z., Oshidari, R., Masai, H. and Yankulov, K.Y.
  • Journal Title: Nucleic Acids Res. Volume: 41 Issue: 18 Pages: 8475-8488
  • DOI: 10.1093/nar/gkt623
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Replication timing regulation of eukaryotic replicons: Rif1 as a global regulator of replication timing. (2013)
  • Author(s): Yamazaki, S. Hayano, M. and Masai, H.
  • Journal Title: Trends in Genetics Volume: 29 Issue: 8 Pages: 449-460
  • DOI: 10.1016/j.tig.2013.05.001
  • Peer Reviewed / Open Access
• [Journal Article] A personal reflection on the Replicon Theory: from R1 plasmid to replication timing regulation in human cells (2013)
  • Author(s): Masai, H.
  • Journal Title: J. Mol. Biol. Volume: 425 Issue: 23 Pages: 4663-4672
  • DOI: 10.1016/j.jmb.2013.03.039
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Journal Article] Regulation of chromosome dynamics by Hsk1 kinase (2013)
  • Author(s): Matsumoto, S. and Masai, H.
  • Journal Title: Biochemical Society Transactions Volume: 41 Issue: 6 Pages: 1712-1719
  • DOI: 10.1042/bst20130217
  • Peer Reviewed / Open Access / Acknowledgement Compliant
• [Presentation] Interaction with G-quadruplex structures forms a basis for Rif1-mediated regulation of DNA replication, transcription and chromatin architecture (2015)
  • Author(s): 正井 久雄、加納 豊、松本 清治、覺正 直子、深津 理乃、森山 賢治、河野 暢明、飯田 啓介、長澤 和夫、増田 晃士、Claire Renard-Guillet、白髭 克彦、山崎 聡志、吉沢 直子
  • Organizer: BMB2015
  • Place of Presentation: 神戸国際会議場（兵庫県神戸市）
  • Year and Date: 2015-12-01
  • Int'l Joint Research / Invited
• [Presentation] Roles of G-quadruplex structures in regulation of DNA replication. (2015)
  • Author(s): Hisao Masai, Yutaka Kanoh, Taku Tanaka, Kenji Moriyama, Yumika Seki, Seiji Matsumoto, Rino Fukatsu, Naoko Kakusho, Satoshi Yamazaki, Yumeka Matsushima, Naoko Yoshizawa, Keisuke Iida, Kazuo Nagasawa
  • Organizer: Cold Spring Harbor Meeting EUKARYOTIC DNA REPLICATION & GENOME MAINTENANCE
  • Place of Presentation: Cold Spring Harbor, New York,USA
  • Year and Date: 2015-09-01
  • Int'l Joint Research / Invited
• [Presentation] Interaction of Rif1 and G-quadruplex forms a basis of Rif1-mediated chromatin regulation. (2015)
  • Author(s): Hisao Masai, Rino Fukatsu, Naoko Kakusho, Yutaka Kanoh, Kenji Moriyama
  • Organizer: The 8th international fission yeast meeting (Pombe2015)
  • Place of Presentation: 神戸国際会議場（兵庫県神戸市）
  • Year and Date: 2015-06-21
  • Int'l Joint Research / Invited
• [Presentation] ゲノムDNA複製制御のメカニズム：生物種を超えた統一像と多様性 (2014)
  • Author(s): 正井 久雄
  • Organizer: 第37回日本分子生物学会年会 (パシフィコ横浜)ワークショップ
  • Place of Presentation: パシフィコ横浜（神奈川）
  • Year and Date: 2014-11-25 – 2014-11-27
  • Invited
• [Presentation] Regulation of mammalian Mcm helicase complexes, (2014)
  • Author(s): Hisao Masai, You Zhiying, Koji L. Ode, Naoko Kakusho, Rino Fukatsu, and Haruhiko Takisawa
  • Organizer: 第87回日本生化学会大会シンポジウム「ゲノムを支えるDNAヘリカーゼの動態を探求する新たな研究展開」
  • Place of Presentation: 国立京都国際会館（京都）
  • Year and Date: 2014-10-15 – 2014-10-18
  • Invited
• [Presentation] 染色体DNA複製プログラムの制御機構 (2014)
  • Author(s): 正井 久雄
  • Organizer: 大阪大学蛋白質研究所セミナー「染色体伝承の分子背景：複製から染色体分離まで」
  • Place of Presentation: 大阪大学（大阪）
  • Year and Date: 2014-09-25 – 2014-09-26
  • Invited
• [Presentation] Regulation of DNA replication program in fission yeast and human cells (2014)
  • Author(s): Hisao Masai
  • Organizer: Marco Foiani（Italy, Milan）教授の招聘により IFOM Foundation – F.I.R.C. Institute of Molecular Oncology Foundationで講演
  • Place of Presentation: Italia, Milan
  • Year and Date: 2014-09-16
  • Invited
• [Presentation] Mrc1/Claspinの分子内相互作用による活性制御および新規機能 (2014)
  • Author(s): 正井 久雄
  • Organizer: 九州大学 大学院薬学研究院 招聘研究セミナー
  • Place of Presentation: 九州大学（福岡）
  • Year and Date: 2014-08-29
  • Invited
• [Presentation] Regulation of replication program in fission yeast and human cells. (2014)
  • Author(s): Hisao Masai
  • Organizer: Peking University（特別招聘講演）
  • Place of Presentation: Peking University（中国）
  • Year and Date: 2014-05-16
  • Invited
• [Presentation] "染色体DNA複製プログラムの制御機構と起源・進化" (2014)
  • Author(s): 正井 久雄、田中 卓、加納 豊、山崎 聡志、松本 清治、吉沢 直子、松嶋 夢叶
  • Organizer: The 2nd Symposium of Cell Cycle Control and Cell Fate (第２回 細胞周期制御と細胞運命 シンポジウム)（招待特別講演）
  • Place of Presentation: 浜松
  • Invited
• [Presentation] "Control of origin firing timing in fission yeast cells" (2013)
  • Author(s): Hisao Masai
  • Organizer: EMBO Conference "Pombe 2013: 7th International Fission Yeast Meeting"
  • Place of Presentation: London UK
  • Invited
• [Presentation] Introductory Remarks (2013)
  • Author(s): Hisao Masai
  • Organizer: 86th Annual Meeting of the Japanese Biochemical Society
  • Place of Presentation: 福岡
  • Invited
• [Presentation] “Chromatin architecture that regulates replication timing of eukaryotic chromosomes.” (2013)
  • Author(s): Hisao Masai, Yutaka Kanoh, Satoshi Yamazaki, Motoshi Hayano, Naoko Yoshizawa, Kenji Moriyama, Yumeka Matsushima, Naoko Kakusho, and Rino Fukatsu
  • Organizer: 第86回日本生化学会大会事務局 インターナショナルセッション『Assembly and architecture of protein complexes regulating inheritance and stable maintenance of genome』
  • Place of Presentation: 福岡
  • Invited
• [Presentation] レプリコン仮説５０周年 (2013)
  • Author(s): 正井 久雄
  • Organizer: 第36回（2013年）日本分子生物学会年会，ワークショップ 『レプリコン仮説50周年：染色体複製装置の形成とその活性の時空間制御』
  • Place of Presentation: 福岡
  • Invited
• [Presentation] "Rif1: a potential global regulator of DNA replication, DNA repair, and recombination." (2013)
  • Author(s): 正井 久雄、山崎 聡志、Lai Mongsing、Foiani Marco、吉沢 直子、加納 豊、松本 清治、森山賢治、覺正 直子、深津 理乃、松嶋 夢叶、河野 暢明、Renard-Guillet Claire
  • Organizer: 第36回（2013年）日本分子生物学会年会，ワークショップ 『DNA二重鎖切断のend-resectionと修復機構の選択・制御』
  • Place of Presentation: 福岡
  • Invited
• [Book] The Initiation of DNA Replication in Eukaryotes "Rif1, a conserved chromatin factor regulating DNA replication, DNA repair and transcription." (2015)
  • Author(s): Naoko Yoshizawa, Satoshi Yamazaki, and *Hisao Masai
  • Total Pages: 623
  • Publisher: Springer
• [Book] DNA Replication, Recombination, and Repair "DNA Replication Timing: Temporal and Spatial Regulation of Eukaryotic DNA Replication." (2015)
  • Author(s): Hayano, M., Matsumoto, S. and *Masai, H.
  • Total Pages: 555
  • Publisher: Springer
• [Book] DNA Replication, Recombination and Repair: Molecular Mechanisms and Pathology (2015)
  • Author(s): Motoshi Hayano, Seiji Matsumoto and Hisao Masai
  • Publisher: Springer